Single cell heterogeneity in tumour suppression and ageing

A recent milestone in the quest for biomarkers relating to ageing was the development of an epigenetic clock by Steve Horvath. It can predict chronological age based on the hyper or hypomethylation of 353 specific CpGs which correlate strongly with age. Acceleration of epigenetic age in blood has been shown to reflect increased mortality and the known early onset of ageing in Down's syndrome patients, which suggests that epigenetic age might be used as a measurement for biological age. With ageing being the biggest risk factor for cancer, cardiovascular and neurodegenerative diseases, the ability to measure biological ageing would present invaluable progress as it would, for the first time, allow the test of interventions to decelerate ageing in a systemic rather than disease specific way (see Aim 3). However, there are major challenges and questions that we need to address:
Aim 1: Making a high-throughput epigenetic clock
Analysing epigenetic age using large methylation arrays is still an expensive method and requires a large amount of starting material (i.e. DNA), which poses an obstacle for its inclusion in many large cohort studies or small molecule screening efforts (see Aim 3). We are developing a minimised version of the original Horvath clock, measuring methylation levels of 18 rather than 353 CpGs. Our method is based on molecular inversion probes and Illumina sequencing which allows easy multiplexing of 96 samples. We use unique molecular identifiers, and achieve an on target rate of over 90% on average. Most importantly, by combining the immense high-throughput of next generation sequencing with the limited number of genomic loci needed for epigenetic age prediction, our method will run at a fraction of the cost of a methylation array.
Aim 2: What is the mechanism behind the epigenetic clock?
While it is clear that the epigenetic clock performs well as an accurate age predictor, what is unclear is whether these epigenetic markers have a direct functional relationship with ageing. Or is the methylation status of these sites simply a coincidental bi-product of ageing or another separate process (most probably epigenetic) relating to ageing? The high-throughput clock will make it easier to find out if these CpGs are involved in epigenetic pathways of the cell. An epigenetic characterisation of the high-throughput clock could also be made which will illuminate us to the physical context of these CpGs, i.e. are they enriched in heterochromatin or near other key epigenetic markers?
Aim 3: Find interventions that affect age acceleration
Age acceleration is the difference between the epigenetic age and the chronological age of a particular sample. Age acceleration varies greatly depending on the tissue type the sample is taken from i.e. some tissues appear to predict age more accurately than others. If compounds are found that can either increase or decrease age acceleration, then they could be applied to a cell model. If there are phenotypic changes that result by manually increasing or decreasing epigenetic age, this would mean the epigenetic clock has a physiological role in the cell, and could open up possibilities towards age related therapies. It would also be an important step in understanding why epigenetic age varies between tissue types, and may also give a clue as to how the epigenetic clock ticks over time.